Non-coding RNAs include structural RNAs (transfer RNA [tRNA] and ribosomal RNA [rRNA]) and small RNAs (sRNAs). They have been mapped by a combination of tiling arrays and RNA-seq with the prediction of transcription start sites.
See also Guell M et al. (2009) Transcriptome Complexity in a Genome-Reduced Bacterium. Science 326 (5957):1268-1271.

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